Welcome to the GrameneMart Tutorial Gramene v. 26 Welcome to the GrameneMart Tutorial A tool for batch data sequence retrieval Select a Gramene dataset to search against. Add filters to the dataset to increase its specificity. Choose the fields to include in the report. Generate a batch report in a format that can be imported into local tools, such as Excel. 5/7/2019

Tutorial Tips If you are viewing this tutorial with Adobe Acrobat Reader, click the “pages” on the left hand side of the Reader for easier navigation. Note! Although we continually work to make Gramene compatible with all browsers, there are problems with some browser versions. If you're having difficulty viewing Gramene, try using a different browser. Please report any problems with browsers through Gramene Feedback. 5/7/2019

GrameneMart is based upon BioMart. The “Mart” tool is particularly suited for providing the 'data mining like” searches of complex descriptive (e.g. biological) data, and is optimized for large databases, such as genomic sequence or microarray experiments. BioMart software is completely Open Source, licensed under the LGPL, and freely available to anyone without restrictions 5/7/2019

Results can be downloaded GrameneMart Built upon BioMart, GrameneMart allows you to search the genes from many of the available genomes at Gramene. These genes can be filtered by chromosome or region, as well as other gene and protein data available for these genes. Results can be downloaded 5/7/2019

Gramene Home Page Click here to open GrameneMart Home Page 5/7/2019 On the Gramene Home Page (www.gramene.org) click on “GrameneMart” on the upper Gramene Navigation Bar to open the Mart Home Page. 5/7/2019

Select a dataset 1) Select a database for this query, and the datasets will open up. In the first stage of the wizard the user is must select, from a drop down menu which dataset he/she would like to query. Once the dataset as been chosen the user must hit the 'Next' button to continue to the Filter stage. Select a dataset for this query, these are the available datasets within the database you selected.. 5/7/2019

Default results options may display here under “Attributes” “Count” After selecting your dataset, you may need to wait a few moments for this page to load. Click the “Count” button at any point to see how many results you have. Clicking on Count as you apply each filter will update the summary . You have the whole dataset of 58406 Oryza sativa japonica genes, because no filters have been applied at this point. Click “Filters” to see your options (next slide) Default results options may display here under “Attributes” 5/7/2019

Formulate the Filters: After each filter selection click on “Count” to update your summary, but remain on the filter page. Formulate the Filters: Remember the summary shows the number of records matching your query and filters. Continue to add filters until the number becomes a manageable size. The filter page contains different types of filters to narrow your query. To include a filter click on the “expand icon” to open the section and select the options of your choice. Notice that the summary panel, on the right, gives information on the current state of the query - the chosen dataset, filters that have been set and attributes that have been selected. Click on the expand icon in front of a filter to open that category to be able to apply aspects of that filter. 5/7/2019

Formulate the Filters: Optionally Filter by Region 1 - For example - select the region of your choice Filter by Region - It is possible to retrieve data from the entire genome, an entire chromosome or a region on a particular chromosome. A region can be defined by chromosomal coordinates (entered as bases, or with the appropriate suffix, as kb or Mb), by two markers or by chromosomal bands. If you intend to limit the selection at the FILTER stage to a particular set of gene identifiers, you should select 'entire genome' as the region, if appropriate. To do this, simply do not select any chromosome or other region option. 2 - Then click on “count” to update your summary. There are 4198 genes on chromosome 12 of the Oryza sativa japonica genome. 5/7/2019

Formulate the Filters: Optionally Filter by Region You can search for all genes between two individual BasePairs You can search for all genes on one or more FPContigs 5/7/2019

Formulate the Filters: Optionally Filter by Gene If you wish to filter by these criteria, select the box and enter specific data Remember: To include a filter click on the square box to the left of the filter name in order to 'check it‘, set the specifics of the filter, and refresh. Filter by Gene. Use the 'Browse' button in the bottom right corner to import values from a file. Simply click on 'Browse' and choose the file to be imported in the open file dialog box that appears. The search can also be limited to genes with a a specific transcript count. Import values from a file 5/7/2019

Formulate the Filters: Optionally Filter by Gene Ontology If you wish to filter by gene ontology, select the box and enter specific data Remember: To include a filter click on the square box to the left of the filter name in order to 'check it‘, set the specifics of the filter, and refresh. Gene Ontology - GO terms can be included to limit the scope of the search, either by evidence codes (useful to pinpoint IEA or 'Inferred from Electronic Annotation') or by limiting the search to specific biological ontologies. '’Browse” button -clicking this button opens up a browser window to QuickGo, where you can browse through the EBI database and find the information you need. Copy and paste the information into the filter box. Use the ‘browse” button to go to EBI’s QuickGO to find your GO term (see next slide). Then click on “count” to update your summary. There are 23 genes on chromosome 12 of with our selected ontology. 5/7/2019

QuickGO You should be on the ontology you entered from Browse to find most appropriate term. (Click a term to see it’s child terms) Note the term ID of choice (copy) and return to filter page (paste). Or use the search function

Formulate the Filters: Optionally Filter by Species Homologs Remember: To include a filter click on the square box to the left of the filter name in order to 'check it‘, set the specifics of the filter, and refresh. Multi species comparisons - Orthologous genes (only or excluded) can now be retrieved. If you wish to compare with other available species, select the box and indicate whether to compare only or exclude that species. 5/7/2019

Formulate the Filters: Optionally Filter by Protein Information Remember: To include a filter click on the square box to the left of the filter name in order to 'check it‘‘, set the specifics of the filter, and refresh. Protein - A number or options allow you to limit the search to specific proteins or specific type domain If you wish to filter by protein, select the box, make a selection from the drop down menu and enter specific data Use the Choose File button to import values from a file 5/7/2019

Formulate the Filters: Optionally Filter by SNP information 5/7/2019

After Filtering, go to Attributes Output fields can be selected from Features, Structures, SNPs, Homologs or Sequences. Select to navigate between them. Each type must be run individually. Gene Features - A series of options define which data should be included in the gene list. Note that these options do not affect the number of genes in the list, but define the details to be included for each item. Note that a gene will be repeated in the list, producing extra rows of output, when several attributes in a particular category apply.Various output formats can be selected, including HTML (with the advantage of linking back to Ensembl GeneView diplays of the individual genes included in the list) and Excel (for convenient processing).･ After your output is a manageable size, click on “Attributes” to select your output options 5/7/2019

Attributes - Features Features: A series of options define which data should be included in your results. Similarly, various output formats can be selected, including HTML and Excel. When you are happy with the query you can preview the results by clicking the Results button (see next slide) Select output options you want by clicking on the box to the left of an option to check it. Selected items will show in summary table.

Hyperlinks to Genome data By default this shows the first 10 results in hyper-linked HTML format but the number and format can be altered using the drop downs above this preview. Results -Features If you want to save your results, options in the top section of the page allow you to select an export format. In addition you can choose to show unique results in cases where there is redundancy due to the data model but note this can affect how long it takes to retrieve your results. Hyperlinks to Genome data 5/7/2019

Export Results Note for particularly intensive queries server time-outs can be a problem, in which case use one of the Web file options. HTML is web-page format, with active links to Genomes data CSV - comma separated values TSV - Tab separated values XLS - excel file ADF - 5/7/2019

Query Script A summary of your current query in BioMart Query XML format can be achieved by clicking the XML button on the toolbar. This is useful for people accessing BioMart via the martservice webservices interface. Similarly a BioMart perl API script to run the same query can be generated by clicking the Perl button.For more detailed help please see the documentation at www.biomart.org. 5/7/2019

Attributes - Structures In addition to Features, there are other output options. And results can be viewed in different formats and numbers of results. 5/7/2019

Attributes - SNPs An example of options and results for SNPs Options to retrieve gene structure information. Options vary with Output type 5/7/2019

Attributes - Homologs An example of options for homologs Options vary with attribute type 5/7/2019

Attributes - Sequences An example of options for Sequences. The diagram will have you’re the area of your option highlighted in red. 5/7/2019

Click on “help” for help document Help file Click on “help” for help document 5/7/2019

FAQ Use Feedback to ask a question Search FAQ FAQs may be able to answer some of your questions. Click on a question or FAQ section to open and close the information. 5/7/2019

For Further Information Data mining using EnSmart (oriented towards human data mining at Ensembl) www.ensembl.org/Homo_sapiens/helpview?se=1;kw=martview BioMart documents www.biomart.org/install.html 5/7/2019

Email Gramene users at gramene@gramene.org Contact Gramene Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene. or Email Gramene users at gramene@gramene.org 5/7/2019